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Publications relevant to gene targeting with ZFN:

  1. Beumer K, Bhattacharyya G, Bibikova M, Trautman JK, Carroll D. Efficient gene targeting in Drosophila with zinc-finger nucleases.
    Genetics. 2006 Apr;172(4):2391-403. Epub 2006 Feb 1.
  1. Porteus MH, Carroll D. Gene targeting using zinc finger nucleases. Nat Biotechnol. 2005 Aug;23(8):967-73. Review.
  1. Carroll D. Using nucleases to stimulate homologous recombination. Methods Mol Biol. 2004;262:195-207. Review.
  1. Bibikova, M., Beumer, K., Trautman, J.K. and Carroll, D. (2003). Enhancing gene targeting with designed zinc-finger nucleases. Science 300: 764.
  2. Bibikova M, Golic M, Golic K, Carroll D (2002) Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics 161: 1169-75.
  3. Bibikova M, Carroll D, Segal DJ, Trautman JK, Smith J, Kim Y-G, Chandrasegaran S (2001) Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Mol. Cell. Biol. 21:289-297
  4. Smith J, Bibikova M, Whitby FG, Reddy AR, Chandrasegaran S, Carroll D (2000) Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains. Nucleic Acids Res. 28:3361-3369
  5. Christensen S, Pont-Kingdon G, Carroll D (2000) Target specificity of the endonuclease from the Xenopus laevis non-LTR retrotransposon, Tx1L. Mol. Cell. Biol. 20:1219-1226
  6. Faruqi AF, Datta HJ, Carroll D, Seidman MM, Glazer PM (2000) Triple helix formation induces recombination in mammalian cells via a nucleotide excision repair-dependent pathway. Mol. Cell. Biol. 20:990-1000
  7. Carroll D (1999) DNA recombination and repair in Xenopus oocytes and eggs: substrate design, direct microinjection, and extract preparation. In A Comparative Methods Approach to the Study of Oocytes and Embryos, JD Richter, ed., Oxford University Press, New York, pp. 173-195
  8. Bibikova M, Wu B, Chi E, Kim K-H, Trautman JK, Carroll D (1998) Characterization of FEN-1 from Xenopus laevis. cDNA cloning and role in DNA metabolism. J. Biol. Chem. 273:34222-34229
  9. Carroll D (1998) Modes of DNA repair in Xenopus oocytes, eggs and extracts. In DNA Damage and Repair — Biochemistry, Genetics and Cell Biology, MF Hoekstra and JA Nickoloff, eds, vol. 1, DNA Repair in Prokaryotes and Lower Eukaryotes, Humana Press, pp. 597-616
  10. Carroll D (1996) Homologous genetic recombination in Xenopus: mechanism and implications for gene manipulation. Prog. Nucleic Acid Res. Mol. Biol. 54:101-125

References

Past publications from the Carroll lab:

  1. Pont-Kingdon, G., Chi, E. and Carroll, D. An L1 retrotransposon from Xenopus laevis and a conserved coiled-coil motif in all L1 elements. Submitted for publication.

  2. Christensen, S., Pont-Kingdon, G. and Carroll, D. (2001). Comparative studies of the endonucleases from two related Xenopus laevis Retrotransposons, Tx1L and Tx2L: Target site specificity and evolutionary implications. Genetica 110: 245-256.

  3. Christensen, S., Pont-Kingdon, G. and Carroll, D. (2000). Target specificity of the endonuclease from the Xenopus laevis non-LTR retrotransposon, Tx1L. Mol. Cell. Biol. 20, 1219-1226.
  4. Pont-Kingdon, G., Chi, E., Christensen, S. and Carroll, D. (1998). RNA expression from a site-specific non-LTR retrotransposon microinjected into Xenopus oocytes. Genetica, 104: 67-76.
  5. Bibikova, M., Wu, B., Chi, E., Kim, K.-H., Trautman, J.K. and Carroll, D. (1998). Characterization of FEN-1 from Xenopus laevis. cDNA cloning and role in DNA metabolism. J. Biol. Chem. 273: 34222-34229.
  6. Segal, D.J., Faruqi, A.F., Glazer, P.M. and Carroll, D. (1997). Processing of targeted psoralen crosslinks in Xenopus oocytes. Mol. Cell. Biol. 17, 6645-6652.
  7. Pont-Kingdon, G., Chi, E., Christensen, S. and Carroll, D. (1997). Ribonucleoprotein formation by the ORF1 protein of the non-LTR retrotransposon Tx1L in Xenopus oocytes. Nucleic Acids Res. 25, 3088-3094.
  8. Segal, D.J. and Carroll, D. (1995). Endonuclease-induced, targeted homologous extrachromosomal recombination in Xenopus oocytes. Proc. Natl. Acad. Sci. USA 92, 806-810.
  9. Lehman, C.W., Jeong-Yu, S., Trautman, J.K. and Carroll, D. (1994). Repair of heteroduplex DNA in Xenopus laevis oocytes. Genetics 138, 459-470.
  10. Carroll, D., Lehman, C.W., Jeong-Yu, S., Dohrmann, P., Dawson, R.J. and Trautman, J.K. (1994). Distribution of exchanges upon homologous recombination of exogenous DNA in Xenopus laevis oocytes. Genetics 138, 445-457.
  11. Lehman, C.W., Trautman, J.K. and Carroll, D. (1994). Illegitimate recombination in Xenopus: Characterization of the end-joined junctions. Nucleic Acids Res. 22, 434-442.
  12. Lehman, C.W., Clemens, M., Worthylake, D.K., Trautman, J.K. and Carroll, D. (1993). Homologous and illegitimate recombination in developing Xenopus oocytes and eggs. Mol. Cell. Biol. 13, 6897-6906.
  13. Lehman, C.W. and Carroll, D. (1993). Isolation of large quantities of functional, cytoplasm-free Xenopus laevis oocyte nuclei. Anal. Biochem. 211, 311-319.
  14. Pont-Kingdon, G., Dawson, R.J. and Carroll, D. (1993). Intermediates in extrachromosomal homologous recombination in Xenopus laevis oocytes: Characterization by electron microscopy. EMBO J. 12, 23-34.
  15. Jeong-Yu, S., and Carroll, D. (1992). The effect of terminal nonhomologies on homologous recombination in Xenopus laevis oocytes. Mol. Cell. Biol. 12, 5426-5437.
  16. Jeong-Yu, S., and Carroll, D. (1992). Test of the double-strand-break repair model of recombination in Xenopus laevis oocytes. Mol. Cell. Biol. 12, 112-119.
  17. Lehman, C.W., and Carroll, D. (1991). Homologous recombination catalyzed by a nuclear extract from Xenopus oocytes. Proc. Natl. Acad. Sci. USA 88, 10840-10844.
  18. Maryon, E., and Carroll, D. (1991). Characterization of recombination intermediates from DNA injected into Xenopus laevis oocytes: Evidence for a nonconservative mechanism of homologous recombination. Mol. Cell. Biol. 11, 3278-3287.
  19. Maryon, E., and Carroll, D. (1991). Involvement of single-stranded tails in homologous recombination of DNA injected into Xenopus laevis oocyte nuclei. Mol. Cell. Biol. 11, 3268-3277.
  20. Urnes, M.S., and Carroll, D. (1990). Amylase synthesis as a simple model system for translation and hybrid arrest in Xenopus oocytes. Gene 95, 267-274.
  21. Sweigert, S.E., and Carroll, D. (1990). Repair and recombination of X-irradiated plasmids in Xenopus laevis oocytes. Mol. Cell. Biol. 10, 5849-5856.
  22. Maryon, E.B., and Carroll, D. (1989). Degradation of linear DNA by a strand-specific exonuclease activity in Xenopus laevis oocytes. Mol. Cell. Biol. 9, 4862-4871.
  23. Garrett, J.E., Knutzon, D.S., and Carroll, D. (1989). Composite transposable elements in the Xenopus laevis genome. Mol. Cell. Biol. 9, 3018-3027.
  24. Grzesiuk, E., and Carroll, D. (1987). Recombination of DNAs in Xenopus oocytes based on short homologous overlaps. Nucl. Acids Res. 15, 971-985.
  25. Carroll, D., Wright, S.H., Wolff, R., Grzesiuk, E., and Maryon, E.B. (1986). Efficient homologous recombination of linear DNA substrates after injection into Xenopus laevis oocytes. Mol. Cell. Biol. 6, 2053-2061.
  26. Garrett, J.E., and Carroll, D. (1986). Tx1: A transposable element from Xenopus laevis with some unusual properties. Mol. Cell. Biol. 6, 933-941.
  27. Carroll, D., Wright, S.H., Ajioka, R.S., and Hussey, Jr., C.E. (1984). Genetic recombination of Xenopus laevis 5S DNA in bacteria. J. Mol. Biol. 178, 155-172.
  28. Swindle, J., Ajioka, J., Dawson, D., Meyers, R., Carroll, D., and Georgopoulos, C. (1984). The nucleotide sequence of the Escherichia coli K12 nusB (groNB) gene. Nucl. Acids Res. 12, 4977-4985.
  29. Carroll, D., Garrett, J.E., and Lam, B.S. (1984). Isolated clusters of paired tandemly repeated sequences in the Xenopus laevis genome. Mol. Cell. Biol. 4, 254-259.
  30. Carroll, D. (1983). Genetic recombination of bacteriophage l DNAs in Xenopus oocytes. Proc. Natl. Acad. Sci. USA 80, 6902-6906.
  31. Young, D., and Carroll, D. (1983). A regular arrangement of nucleosomes on 5S ribosomal genes in Xenopus laevis. Mol. Cell. Biol. 3, 720-730.
  32. Lam, B.S., and Carroll, D. (1983). Tandemly repeated DNA sequences from Xenopus laevis. II. Clusters of a 388 bp repeating unit. J. Mol. Biol. 165, 587-597.
  33. Lam, B.S., and Carroll, D. (1983). Tandemly repeated DNA sequences from Xenopus laevis. I. Studies on sequence organization and variation in satellite 1 DNA (741 base-pair repeat). J. Mol. Biol. 165, 567-585.
  34. Humphries, S.E., Young, D., and Carroll, D. (1979). The chromatin structure of the 5S RNA genes of Xenopus laevis. Biochemistry 18, 3223-3231.